Season 2:
Yep, GRAVE is no laughing matter. They set out to destroy the cyber world and take over the real one! They release a huge Virus Beast that is deleting navis everywhere. Our heroes head in to help, along with World Three's navis. But the virus beast is too powerful, and the rest of GRAVE's operatives are nothing to be laughed at either... The only navi who seems to stand a chance is a mysterious navi named Bass. Bass kidnaps Megaman and takes some of his memories from the end of the N1. Meanwhile, Net city is being evacuated - and Protoman is deleted!
Getting desperate the gang is forced to team up with World Three and a man called Mr. Famous (who has been helping both World three and Lan fight GRAVE). Mr. Famous gives them the extra code - a powerful, but dangerous weapon. The extra code gives a navi a burst of speed, but drains all their energy in the process. Unless another navi is there to save them... they could be deleted! But Megaman has to use the code to win.
Fighting GRAVE our heroes learn some shocking things. The first is that renowned philanthropist Mr. Gous is actually working for GRAVE - and he's Count Zap's older brother! And the two do not get along at all... Then they learn that Bass is actually what remains of Pharaohman's program and the Virus Beast was created from his data! Both are 'ultimate programs' and are able to regenerate using the discarded data and flaws in the net -even viruses. When Bass discovers the truth (through his 'experience' with Megaman) he sets out to incorporate the Virus Beast back into himself... but he fails. It's all up to Megaman. But he seems to have caught some sort of virus from Bass. It looks suspiciously like the program the Virus Beast is using to consume net city! And it is interfering with his ability to fight. Lan is forced to use the extra code, but Megaman is still losing. This is when Mr. Famous reveals the most shocking thing of all. Megaman 'caught' a bug from Bass that can only be transmitted to and from ultimate programs. Megaman, Protoman, and Bass are all ultimate programs. The bug takes over Megaman and causes him to consume all of net city - including the virus beast. That looks bad, and Megaman is totally unresponsive. It appears as though Lan has lost him again. But then the city begins to rebuild itself, the navi's all return, and Megaman is alright. Seems that, as an ultimate program, he reset the system! Which was the ultimate program's job after all...
Oh, and a few more shocking details... Kid Grave, leader of Grave, turned out to be a robot built and controlled by Mr. Wiley (who was supposed to be dead!). And World Three now runs a curry shop... yeah... talk about strange... Oh! And the World Three navis were all deleted protecting Megaman! *Gasp* How times have changed ^_^